Selected Publications



Byrne LC, Day TP, Visel M, Strazzeri JA, Fortuny C, Dalkara D, Merigan WH, Schaffer D, Flannery JG. In vivo directed evolution of AAV in the primate retina [published online ahead of print, 2020 Apr 9]. JCI Insight. 2020;135112. View PDF.



Berry MH, Holt A, Salari A, Veit J, Visel M, Levitz J, Aghi K, Gaub BM, Siyver B, Flannery JG, Isacoff EY. et al. Restoration of high-sensitivity and adapting vision with a cone opsin. Nat Commun. 2019;10(1):1221. Published 2019 Mar 15. View PDF.



Baker CK, Flannery JG. Innovative Optogenetic Strategies for Vision Restoration. Front Cell Neurosci. 2018;12:316. Published 2018 Sep 21. View PDF.



Fortuny C, Flannery JG. Mutation-Independent Gene Therapies for Rod-Cone Dystrophies. Adv Exp Med Biol. 2018. View Full Text.



Day TP, Byrne LC, Flannery JG, Schaffer DV. Screening for Neutralizing Antibodies Against Natural and Engineered AAV Capsids in Nonhuman Primate Retinas. Methods Mol Biol. 2018;1715:239‐249. View Full Text.



Gaub BM, Berry MH, Visel M, Holt A, Isacoff EY, Flannery JG. Optogenetic Retinal Gene Therapy with the Light Gated GPCR Vertebrate Rhodopsin. Methods Mol Biol. 2018;1715:177‐189. View Full Text.



Rosa JM, Bos R, Sack GS, et al. Neuron-glia signaling in developing retina mediated by neurotransmitter spillover. Elife. 2015;4:e09590.  View PDF.



Gaub BM, Berry MH, Holt AE, Isacoff EY, Flannery JG. Optogenetic Vision Restoration Using Rhodopsin for Enhanced Sensitivity. Mol Ther. 2015;23(10):1562‐1571. View PDF.



Byrne LC, Lin YJ, Lee T, Schaffer DV, Flannery JG. The expression pattern of systemically injected AAV9 in the developing mouse retina is determined by age. Mol Ther. 2015 Feb;23(2):290-6. Epub 2014 Sep 16. View PDF.



Byrne LC, Dalkara D, Luna G, Fisher SK, Clérin E, Sahel JA, Léveillard T, Flannery JG. Viral-mediated RdCVF and RdCVFL expression protects cone and rod photoreceptors in retinal degeneration. J Clin Invest. 2015 Jan;125(1):105-16. Epub 2014 Nov 21. View PDF.



Byrne LC, Oztürk BE, Lee T, Fortuny C, Visel M, Dalkara D, Schaffer DV, Flannery JG. Retinoschisin gene therapy in photoreceptors, Müller glia or all retinal cells in the Rs1h-/- mouse. Gene Ther. 2014 Apr 3. View PDF.



Day TP, Byrne LC, Schaffer DV, Flannery JG. Advances in AAV Vector Development for Gene Therapy in the Retina. Adv Exp Med Biol. 2014;801:687-93. View PDF.



Dalkara D, Byrne LC, Klimczak RR, Visel M, Yin L, Merigan WH, Flannery JG, Schaffer DV. In vivo-directed evolution of a new adeno-associated virus for therapeutic outer retinal gene delivery from the vitreous. Sci Transl Med. 2013 Jun 12;5(189):189ra76. View PubMed.



Flannery JG, Visel M. Adeno-associated viral vectors for gene therapy of inherited retinal degenerations. Methods Mol Biol. 2013;935:351-69. View Full Text.



Byrne LC, Khalid F, Lee T, Zin EA, Greenberg KP, Visel M, Schaffer DV, Flannery JG. AAV-mediated, optogenetic ablation of Müller Glia leads to structural and functional changes in the mouse retina. PLoS One. 2013 Sep 27;8(9):e76075.View PDF.



Dalkara D, Byrne LC, Lee T, Hoffmann NV, Schaffer DV, Flannery JG. Enhanced gene delivery to the neonatal retina through systemic administration of tyrosine-mutated AAV9. Gene Ther. 2012 Feb;19(2):176-81. View PubMed.



Dalkara D, Kolstad KD, Guerin KI, Hoffmann NV, Visel M, Klimczak RR, Schaffer DV, Flannery JG. AAV mediated GDNF secretion from retinal glia slows down retinal degeneration in a rat model of retinitis pigmentosa. Mol Ther. 2011 Sep;19(9):1602-8. View PDF.



Caporale N, Kolstad KD, Lee T, Tochitsky I, Dalkara D, Trauner D, Kramer R, Dan Y, Isacoff EY, Flannery JG. LiGluR restores visual responses in rodent models of inherited blindness. Mol Ther. 2011 Jul;19(7):1212-9. View PDF.



Kolstad KD, Dalkara D, Guerin K, Visel M, Hoffmann N, Schaffer DV, Flannery JG. Changes in adeno-associated virus-mediated gene delivery in retinal degeneration. Hum Gene Ther. 2010 May;21(5):571-8. View PDF.



Dalkara D, Kolstad KD, Caporale N, Visel M, Klimczak RR, Schaffer DV, Flannery JG. Inner limiting membrane barriers to AAV-mediated retinal transduction from the vitreous. Mol Ther. 2009 Dec;17(12):2096-102. View PDF.



Koerber JT, Klimczak R, Jang JH, Dalkara D, Flannery JG, Schaffer DV. Molecular evolution of adeno-associated virus for enhanced glial gene delivery. Mol Ther. 2009 Dec;17(12):2088-95. View PDF.



Klimczak RR, Koerber JT, Dalkara D, Flannery JG, Schaffer DV. A novel adeno-associated viral variant for efficient and selective intravitreal transduction of rat Müller cells. PLoS One. 2009 Oct 14;4(10):e7467. View PDF.



Geller SF, Guerin KI, Visel M, Pham A, Lee ES, Dror AA, Avraham KB, Hayashi T, Ray CA, Reh TA, Bermingham-McDonogh O, Triffo WJ, Bao S, Isosomppi J, Västinsalo H, Sankila EM, Flannery JG. CLRN1 is nonessential in the mouse retina but is required for cochlear hair cell development. PLoS Genet. 2009 Aug;5(8):e1000607. View PDF.



Guerin K, Gregory-Evans CY, Hodges MD, Moosajee M, Mackay DS, Gregory-Evans K, Flannery JG. Systemic aminoglycoside treatment in rodent models of retinitis pigmentosa. Exp Eye Res. 2008 Sep;87(3):197-207. View PubMed.



Geller SF, Ge PS, Visel M, Flannery JG. In vitro analysis of promoter activity in Müller cells. Mol Vis. 2008 Apr 23;14:691-705. View PDF.



Lee ES, Flannery JG. Transport of truncated rhodopsin and its effects on rod function and degeneration. Invest Ophthalmol Vis Sci. 2007 Jun;48(6):2868-76.  View PDF.



Geller SF, Ge PS, Visel M, Greenberg KP, Flannery JG. Functional promoter testing using a modified lentiviral transfer vector. Mol Vis. 2007 May 17;13:730-9. View PDF.



Greenberg KP, Geller SF, Schaffer DV, Flannery JG. Targeted transgene expression in muller glia of normal and diseased retinas using lentiviral vectors. Invest Ophthalmol Vis Sci. 2007 Apr;48(4):1844-52.  View PDF.



Lee ES, Burnside B, Flannery JG. Characterization of peripherin/rds and rom-1 transport in rod photoreceptors of transgenic and knockout animals. Invest Ophthalmol Vis Sci. 2006 May;47(5):2150-60. View PDF.



Flannery JG, Greenberg KP. Looking within for vision. Neuron. 2006 Apr 6;50(1):1-3. Erratum in: Neuron. 2006 Apr 20;50(2):341. View Full Text.



Greenberg KP, Lee ES, Schaffer DV, Flannery JG. Gene delivery to the retina using lentiviral vectors. Adv Exp Med Biol. 2006;572:255-66. View PubMed.



McGee Sanftner LH, Abel H, Hauswirth WW, Flannery JG. Glial cell line derived neurotrophic factor delays photoreceptor degeneration in a transgenic rat model of retinitis pigmentosa. Mol Ther. 2001 Dec;4(6):622-9. Free Full Text.



McGee Sanftner LH, Rendahl KG, Quiroz D, Coyne M, Ladner M, Manning WC, Flannery JG. Recombinant AAV-mediated delivery of a tet-inducible reporter gene to the rat retina. Mol Ther. 2001 May;3(5 Pt 1):688-96. Free Full Text.



Green ES, Rendahl KG, Zhou S, Ladner M, Coyne M, Srivastava R, Manning WC, Flannery JG. Two animal models of retinal degeneration are rescued by recombinant adeno-associated virus-mediated production of FGF-5 and FGF-18. Mol Ther. 2001 Apr;3(4):507-15. Free Full Text.



Lau D, McGee LH, Zhou S, Rendahl KG, Manning WC, Escobedo JA, Flannery JG. Retinal degeneration is slowed in transgenic rats by AAV-mediated delivery of FGF-2. Invest Ophthalmol Vis Sci. 2000 Oct;41(11):3622-33. View PDF.



Green ES, Menz MD, LaVail MM, Flannery JG. Characterization of rhodopsin mis-sorting and constitutive activation in a transgenic rat model of retinitis pigmentosa. Invest Ophthalmol Vis Sci. 2000 May;41(6):1546-53. View PDF.



For  a list of complete work, please visit John’s Google Scholar page.